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Trends in bacterial signalling pathways

Bacterial (and archaeal) signalling systems are remarkably similar to eukaryotic ones. As well as the typical and well described two-component signalling systems (a histadine-kinase sensor which senses a signal and passes this on to a response-regulator) bacteria also contain multi-component systems, for both inter- and intra-cellular signalling.

All cells constantly monitor their external and internal environment in order to effectively exploit their surroundings. Bacteria are no different, and all contain a variety of different signal transduction pathways in order to do this. The distribution of these transduction pathways varies between bacteria, based not just on phylogeny but lifestyle and environment as well. Galperin's study (reference below) looked at the distribution of bacterial signalling systems over 167 different genomes (including some archaea) to examine if there were any overall trends.

The first trend he found was that the number of signal transduction pathways in a genome increases with genome size:

Image taken from reference (1) below

The graph above shows log[protein number] on the y-axis plotted against log[genome size] on the x-axis. There are exceptions, but the overall trend is that the two have a clear linear relationship: the more genes a bacteria has, the more of them it will dedicate to monitoring its internal and external surroundings.

The second trend, which perhaps is not quite such a surprising find, is that the number of signal transduction pathways depends markedly on the surrounding environment. Ruminant bacteria (with a few exceptions) have smaller and simpler transduction pathways, with fewer external signals being reported. In contrast, facultative pathogens, which have diverse ecological niches, will have far more systems for sensing their surroundings. This makes sense, as faculative anaerobes need to respond and react to the different environments in which they find themselves. Ruminant bacteria, which live their whole lives in the gut of ruminant mammals (such as sheep and cattle), only can survive in one environment, so have very little need for sophisticated sensor-response systems.

It was also found that gram negative bacteria have a larger number of signalling systems than gram positive. This may be due to the fact that gram negative bacteria are motile, and therefore need to monitor what kind of environment they are moving into, and how their internal conditions are reacting to the change. It may also have something to do with the difference in cell wall structure. Gram negative cells have two cell membranes, with a glycoprotein layer in the middle (Gram positives are just glycoprotein all the way up) and are therefore more likely to have signalling systems with more than two componants, as the signal in some cases must be transmitted first through the outer membrane, and then through the inner.

As well as looking at responses to extracellular conditions, the study also examined intracellular signalling pathways, the bacterial sensing of its internal conditions. Intracellular pathways followed different trends to extracellular ones, for example free-living archaea were found to have fewer extracellular signaling transduction pathways, but more intracellular ones. Cyanobacteria were found to have the largest number of intracellular pathways. A potential reason for this is that cyanobacteria are the only bacteria that produce oxygen, rather than trying to keep it outside the cell. Oxygen is dangerous, it produces reactive species and affects the overall redox balance inside the cell. Cyanobacteria therefore may need more signalling pathways to keep a close eye on the oxygen inside it's cell.

The study also shows that, despite the evolutionary similarity to eukaryotic systems, there are some unique features within bacterial signalling systems (especially the lesser explored internal cell signalling). Many of these are shared by pathogenic bacteria, offering the potential for another target for bacteriocidal drugs, or at the very least drugs that prevent the growth and invasion of bacteria in the body, allowing the immune system time to safely remove them.

2 comments:

When I first glanced at the title, I thought Cell Press unveiled a new journal dedicated to bacterial signalling pathways...is that bad?

"the more genes a bacteria has, the more of them it will dedicate to monitoring its internal and external surroundings."

Or, those genes involved in signalling have have been duplicated, and subsequently neo- or subfunctionalised. Large genomes tend to be a result of 'degradation', if you will: if there isn't much pressure towards streamlining, then it becomes excusable for an operation that previously required a single gene to be modified to require several.

Interestingly, this seems to be reversed in intracellular parasites, and to some extent, gut endosymbionts as well (but not as much). If you no longer need certain metabolic (or signalling) pathways, they can (and will) go to [evolutionary] hell. The large effective population size in bacterial populations seems to promote streamlining, but it would be interesting if that's the case for all of them -- do you know anything about that?

But I guess the main point is that in the case of large genomes, it's not that the organism now has a shitload more genes to play with, so it sits there and goes "hmmm, where should I invest them?", but the picture is more complex, and reversed: the genomes are larger largely because 'anti-streamlining' gene duplications and the rest of it were tolerated, not the other way around.

Of course, those could later be exapted into something adaptive, but it's hard to see how a pathway duplication + modification can be adaptive initially...

Oooh, and another question for a bacteriologist: what's up with the adherence to the gram-negative vs. gram-positive categorisation? Isn't it horribly polyphyletic and painfully far from constituting any semblance of a natural classification? (then again, I do get most of my knowledge of prokaryotes from Tom Cavalier-Smith's papers, so I don't know what you guys think of his bacterial evolution theories)

I've got more questions, but I'll avoid spamming your blog... >_>

Signalling is fascinating stuff*, so nice post!

*until you have to painfully *memorise* pathways for a very medically-oriented biochem class >.<

Heh, I never thought of the title that way, but it does make sense, considering all the other 'trends' journals :)

ooh...I never thought about gene-duplication in terms of gene size, at least it never occured to me in terms of this paper. It could be a potential way of getting so many signalling systems, and useful duplicates would be hugely selected for by motile bacteria with many environmental pressures.

Obligate intracellular bacterial parasites tend to loose a lot of their genome as well, it's only the ones that can occupy a number of different niches that hang on to them. Andfor the same reason as any other parasites, they simply don't need them.

Gram positive/Gram negative is still used routinely. It's not *wonderfully* evolutionarily taxonomic, but it is still one of the most useful things to know about bacteria. In terms of cell-wall/antibiotic interactions (where I am now) it's one of THE most useful things to know, same with people working on bacterial secretion as well. Even though it's based on a seemingly arbitary staining method the different membrane systems play a major part in how the bacteria will behave.

I really need to look up these "Tom Cavalier-Smith" papers of which you speak...I just seem to have no time at the moment. heh.

(totally agree with you about signalling btw, i find it one of the most difficult areas to study. That's pretty much the reason I looked at this paper, I was hoping that generating interest in bacterial signalling might encourage me to start looking at euk pathways with some kind of enthusiasm)